private static string F_ANGLE_FORMAT(double angle) => angle.ToString("F3", NumberFormatInfo.InvariantInfo).PadLeft(7); //"%3.3f";
public void WriteCrystal(ICrystal crystal)
{
try
{
WriteHeader();
Vector3 a = crystal.A;
Vector3 b = crystal.B;
Vector3 c = crystal.C;
double[] ucParams = CrystalGeometryTools.CartesianToNotional(a, b, c);
writer.Write("CRYST1 " + F_LENGTH_FORMAT(ucParams[0]));
writer.Write(F_LENGTH_FORMAT(ucParams[1]));
writer.Write(F_LENGTH_FORMAT(ucParams[2]));
writer.Write(F_ANGLE_FORMAT(ucParams[3]));
writer.Write(F_ANGLE_FORMAT(ucParams[4]));
writer.Write('\n');
// before saving the atoms, we need to create cartesian coordinates
foreach (var atom in crystal.Atoms)
{
// Debug.WriteLine($"PDBWriter: atom -> {atom}");
// if it got 3D coordinates, use that. If not, try fractional coordinates
if (atom.Point3D == null && atom.FractionalPoint3D != null)
{
Vector3 frac = atom.FractionalPoint3D.Value;
Vector3 cart = CrystalGeometryTools.FractionalToCartesian(a, b, c, frac);
atom.Point3D = cart;
}
}
WriteMolecule(crystal.Builder.NewAtomContainer(crystal));
}
catch (IOException exception)
{
throw new CDKException("Error while writing file: " + exception.Message, exception);
}
}
/// <summary>
/// Determines the features present in the given <see cref="IAtomContainer"/>.
/// </summary>
/// <param name="molecule">IAtomContainer to determine the features off</param>
/// <returns>integer representation of the present features</returns>
public static DataFeatures GetSupportedDataFeatures(IAtomContainer molecule)
{
DataFeatures features = DataFeatures.None;
if (MoleculeFeaturesTool.HasElementSymbols(molecule))
{
features = features | DataFeatures.HasAtomElementSymbol;
}
if (GeometryUtil.Has2DCoordinates(molecule))
{
features = features | DataFeatures.Has2DCoordinates;
}
if (GeometryUtil.Has3DCoordinates(molecule))
{
features = features | DataFeatures.Has3DCoordinates;
}
if (CrystalGeometryTools.HasCrystalCoordinates(molecule))
{
features = features | DataFeatures.HasFractionalCrystalCoordinates;
}
if (MoleculeFeaturesTool.HasFormalCharges(molecule))
{
features = features | DataFeatures.HasAtomFormalCharges;
}
if (MoleculeFeaturesTool.HasPartialCharges(molecule))
{
features = features | DataFeatures.HasAtomPartialCharges;
}
if (MoleculeFeaturesTool.HasGraphRepresentation(molecule))
{
features = features | DataFeatures.HasGraphRepresentation;
}
return(features);
}
private void possiblySetCellParams(double a, double b, double c, double alpha, double beta, double gamma)
{
if (a != 0.0 && b != 0.0 && c != 0.0 && alpha != 0.0 && beta != 0.0 && gamma != 0.0)
{
//logger.info("Found and set crystal cell parameters");
Vector3d[] axes = CrystalGeometryTools.notionalToCartesian(a, b, c, alpha, beta, gamma);
crystal.A = axes[0];
crystal.B = axes[1];
crystal.C = axes[2];
}
}
private void PossiblySetCellParams(double a, double b, double c, double alpha, double beta, double gamma)
{
if (a != 0.0 && b != 0.0 && c != 0.0 && alpha != 0.0 && beta != 0.0 && gamma != 0.0)
{
Trace.TraceInformation("Found and set crystal cell parameters");
var axes = CrystalGeometryTools.NotionalToCartesian(a, b, c, alpha, beta, gamma);
crystal.A = axes[0];
crystal.B = axes[1];
crystal.C = axes[2];
}
}
public void TestReading()
{
var filename = "NCDK.Data.ShelX.frame_1.res";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
ShelXReader reader = new ShelXReader(ins);
Crystal crystal = (Crystal)reader.Read(new Crystal());
reader.Close();
Assert.IsNotNull(crystal);
Assert.AreEqual(42, crystal.Atoms.Count);
var notional = CrystalGeometryTools.CartesianToNotional(crystal.A, crystal.B, crystal.C);
Assert.AreEqual(7.97103, notional[0], 0.001);
Assert.AreEqual(18.77220, notional[1], 0.001);
Assert.AreEqual(10.26222, notional[2], 0.001);
Assert.AreEqual(90.0000, notional[3], 0.001);
Assert.AreEqual(90.0000, notional[4], 0.001);
Assert.AreEqual(90.0000, notional[5], 0.001);
}
public void TestRoundTrip()
{
Crystal crystal = new Crystal();
double a = 3.0;
double b = 5.0;
double c = 7.0;
double alpha = 90.0;
double beta = 110.0;
double gamma = 100.0;
var axes = CrystalGeometryTools.NotionalToCartesian(a, b, c, alpha, beta, gamma);
crystal.A = axes[0];
crystal.B = axes[1];
crystal.C = axes[2];
// serialazing
StringWriter sWriter = new StringWriter();
ShelXWriter resWriter = new ShelXWriter(sWriter);
resWriter.Write(crystal);
resWriter.Close();
string resContent = sWriter.ToString();
// deserialazing
ShelXReader resReader = new ShelXReader(new StringReader(resContent));
ICrystal rCrystal = (ICrystal)resReader.Read(new Crystal());
// OK, do checking
Assert.IsNotNull(rCrystal);
Assert.AreEqual(crystal.A.X, rCrystal.A.X, 0.001);
Assert.AreEqual(crystal.A.Y, rCrystal.A.Y, 0.001);
Assert.AreEqual(crystal.A.Z, rCrystal.A.Z, 0.001);
Assert.AreEqual(crystal.B.X, rCrystal.B.X, 0.001);
Assert.AreEqual(crystal.B.Y, rCrystal.B.Y, 0.001);
Assert.AreEqual(crystal.B.Z, rCrystal.B.Z, 0.001);
Assert.AreEqual(crystal.C.X, rCrystal.C.X, 0.001);
Assert.AreEqual(crystal.C.Y, rCrystal.C.Y, 0.001);
Assert.AreEqual(crystal.C.Z, rCrystal.C.Z, 0.001);
}
private CMLMolecule CDKCrystalToCMLMolecule(ICrystal crystal, bool setIDs)
{
var molecule = CDKAtomContainerToCMLMolecule(crystal, false, false);
var cmlCrystal = new CMLCrystal();
if (useCMLIDs && setIDs)
{
IDCreator.CreateIDs(crystal);
}
if (!string.IsNullOrEmpty(crystal.Id))
{
cmlCrystal.Id = crystal.Id;
}
this.CheckPrefix(cmlCrystal);
cmlCrystal.Z = crystal.Z.Value;
var params_ = CrystalGeometryTools.CartesianToNotional(crystal.A, crystal.B, crystal.C);
Debug.WriteLine($"Number of cell params: {params_.Length}");
cmlCrystal.SetCellParameters(params_);
molecule.Add(cmlCrystal);
return(molecule);
}
private ICrystal ReadCrystal(ICrystal crystal)
{
string line = input.ReadLine();
bool end_found = false;
while (line != null && !end_found)
{
/* is line continued? */
if (line.Length > 0 && line.Substring(line.Length - 1).Equals("=", StringComparison.Ordinal))
{
/* yes, line is continued */
line = line + input.ReadLine();
}
/* determine ShelX command */
string command;
try
{
command = line.Substring(0, 4);
}
catch (ArgumentOutOfRangeException)
{
// disregard this line
break;
}
Debug.WriteLine($"command: {command}");
var u_command = command.ToUpperInvariant();
if (u_command.StartsWith("REM", StringComparison.Ordinal))
{
/* line is comment, disregard */
/* 7.1 Crystal data and general instructions */
}
else if (u_command.StartsWith("END", StringComparison.Ordinal))
{
end_found = true;
}
else
{
switch (u_command)
{
case "TITL":
break;
case "CELL":
{
// example: CELL 1.54184 23.56421 7.13203 18.68928 90.0000
// 109.3799 90.0000 CELL 1.54184 7.11174 21.71704 30.95857
// 90.000 90.000 90.000
var st = Strings.Tokenize(line);
//st[0]; // string command_again
//st[1]; // string wavelength
string sa = st[2];
string sb = st[3];
string sc = st[4];
string salpha = st[5];
string sbeta = st[6];
string sgamma = st[7];
Debug.WriteLine($"a: {sa}");
Debug.WriteLine($"b: {sb}");
Debug.WriteLine($"c: {sc}");
Debug.WriteLine($"alpha: {salpha}");
Debug.WriteLine($"beta : {sbeta}");
Debug.WriteLine($"gamma: {sgamma}");
double a = FortranFormat.Atof(sa);
double b = FortranFormat.Atof(sb);
double c = FortranFormat.Atof(sc);
double alpha = FortranFormat.Atof(salpha);
double beta = FortranFormat.Atof(sbeta);
double gamma = FortranFormat.Atof(sgamma);
Vector3[] axes = CrystalGeometryTools.NotionalToCartesian(a, b, c, alpha, beta, gamma);
crystal.A = axes[0];
crystal.B = axes[1];
crystal.C = axes[2];
}
break;
case "ZERR":
case "LATT":
case "SYMM":
case "SFAC":
case "DISP":
case "UNIT":
case "LAUE":
case "REM ":
case "MORE":
case "TIME":
/* 7.2 Reflection data input */
case "HKLF":
case "OMIT":
case "SHEL":
case "BASF":
case "TWIN":
case "EXTI":
case "SWAT":
case "HOPE":
case "MERG":
/* 7.3 Atom list and least-squares constraints */
case "SPEC":
case "RESI":
case "MOVE":
case "ANIS":
case "AFIX":
case "HFIX":
case "FRAG":
case "FEND":
case "EXYZ":
//case "EXTI":
case "EADP":
case "EQIV":
/* 7.4 The connectivity list */
case "CONN":
case "PART":
case "BIND":
case "FREE":
/* 7.5 Least-squares restraints */
case "DFIX":
case "DANG":
case "BUMP":
case "SAME":
case "SADI":
case "CHIV":
case "FLAT":
case "DELU":
case "SIMU":
case "DEFS":
case "ISOR":
case "NCSY":
case "SUMP":
/* 7.6 Least-squares organization */
case "L.S.":
case "CGLS":
case "BLOC":
case "DAMP":
case "STIR":
case "WGHT":
case "FVAR":
/* 7.7 Lists and tables */
case "BOND":
case "CONF":
case "MPLA":
case "RTAB":
case "HTAB":
case "LIST":
case "ACTA":
case "SIZE":
case "TEMP":
case "WPDB":
/* 7.8 Fouriers, peak search and lineprinter plots */
case "FMAP":
case "GRID":
case "PLAN":
break;
case "MOLE":
/* NOT DOCUMENTED BUT USED BY PLATON */
break;
case "SPGR":
{
// Line added by PLATON stating the spacegroup
var st = Strings.Tokenize(line);
//st[0]; // string command_again
string spacegroup = st[1];
crystal.SpaceGroup = spacegroup;
}
break;
case " ":
{
Debug.WriteLine($"Disrgarding line assumed to be added by PLATON: {line}");
/* All other is atom */
}
break;
default:
{
//Debug.WriteLine($"Assumed to contain an atom: {line}");
// this line gives an atom, because all lines not starting with
// a ShelX command is an atom (that sucks!)
var st = Strings.Tokenize(line);
string atype = st[0];
//st[1]; // string scatt_factor
string sa = st[2];
string sb = st[3];
string sc = st[4];
// skip the rest
if (char.IsDigit(atype[1]))
{
// atom type has a one letter code
atype = atype.Substring(0, 1);
}
else
{
var sb2 = new StringBuilder();
sb2.Append(atype[1]);
atype = atype.Substring(0, 1) + sb2.ToString().ToLowerInvariant();
}
double[] frac = new double[3];
frac[0] = FortranFormat.Atof(sa); // fractional coordinates
frac[1] = FortranFormat.Atof(sb);
frac[2] = FortranFormat.Atof(sc);
Debug.WriteLine("fa,fb,fc: " + frac[0] + ", " + frac[1] + ", " + frac[2]);
if (string.Equals(atype, "Q", StringComparison.OrdinalIgnoreCase))
{
// ingore atoms named Q
}
else
{
Trace.TraceInformation("Adding atom: " + atype + ", " + frac[0] + ", " + frac[1] + ", " + frac[2]);
IAtom atom = crystal.Builder.NewAtom(atype);
atom.FractionalPoint3D = new Vector3(frac[0], frac[1], frac[2]);
crystal.Atoms.Add(atom);
Debug.WriteLine($"Atom added: {atom}");
}
}
break;
}
}
line = input.ReadLine();
}
return(crystal);
}
private string ProcessAtomLoopBlock(string firstLine)
{
int atomLabel = -1; // -1 means not found in this block
int atomSymbol = -1;
int atomFractX = -1;
int atomFractY = -1;
int atomFractZ = -1;
int atomRealX = -1;
int atomRealY = -1;
int atomRealZ = -1;
string line = firstLine.Trim();
int headerCount = 0;
bool hasParsableInformation = false;
while (line != null && line[0] == '_')
{
headerCount++;
if (line.Equals("_atom_site_label", StringComparison.Ordinal) || line.Equals("_atom_site_label_atom_id", StringComparison.Ordinal))
{
atomLabel = headerCount;
hasParsableInformation = true;
Trace.TraceInformation($"label found in col: {atomLabel}");
}
else if (line.StartsWith("_atom_site_fract_x", StringComparison.Ordinal))
{
atomFractX = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("frac x found in col: " + atomFractX);
}
else if (line.StartsWith("_atom_site_fract_y", StringComparison.Ordinal))
{
atomFractY = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("frac y found in col: " + atomFractY);
}
else if (line.StartsWith("_atom_site_fract_z", StringComparison.Ordinal))
{
atomFractZ = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("frac z found in col: " + atomFractZ);
}
else if (string.Equals(line, "_atom_site.Cartn_x", StringComparison.Ordinal))
{
atomRealX = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("cart x found in col: " + atomRealX);
}
else if (string.Equals(line, "_atom_site.Cartn_y", StringComparison.Ordinal))
{
atomRealY = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("cart y found in col: " + atomRealY);
}
else if (string.Equals(line, "_atom_site.Cartn_z", StringComparison.Ordinal))
{
atomRealZ = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("cart z found in col: " + atomRealZ);
}
else if (string.Equals(line, "_atom_site.type_symbol", StringComparison.Ordinal))
{
atomSymbol = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("type_symbol found in col: " + atomSymbol);
}
else
{
Trace.TraceWarning("Ignoring atom loop block field: " + line);
}
line = input.ReadLine().Trim();
}
if (!hasParsableInformation)
{
Trace.TraceInformation("No parsable info found");
return(SkipLoopBody(line));
}
else
{
// now that headers are parsed, read the data
while (line != null && line.Length > 0 &&
line[0] != '#' &&
line[0] != '_' &&
!line.StartsWith("loop_", StringComparison.Ordinal) &&
!line.StartsWith("data_", StringComparison.Ordinal))
{
Debug.WriteLine("new row");
var tokenizer = Strings.Tokenize(line);
if (tokenizer.Count < headerCount)
{
Trace.TraceWarning("Column count mismatch; assuming continued on next line");
Debug.WriteLine($"Found #expected, #found:{headerCount}, {tokenizer.Count}");
tokenizer = Strings.Tokenize(line + input.ReadLine());
}
int colIndex = 0;
// process one row
IAtom atom = crystal.Builder.NewAtom("C");
Vector3 frac = new Vector3();
Vector3 real = new Vector3();
bool hasFractional = false;
bool hasCartesian = false;
foreach (var field in tokenizer)
{
colIndex++;
Debug.WriteLine("Parsing col,token: " + colIndex + "=" + field);
if (colIndex == atomLabel)
{
if (atomSymbol == -1)
{
// no atom symbol found, use label
string element = ExtractFirstLetters(field);
atom.Symbol = element;
}
atom.Id = field;
}
else if (colIndex == atomFractX)
{
hasFractional = true;
frac.X = ParseIntoDouble(field);
}
else if (colIndex == atomFractY)
{
hasFractional = true;
frac.Y = ParseIntoDouble(field);
}
else if (colIndex == atomFractZ)
{
hasFractional = true;
frac.Z = ParseIntoDouble(field);
}
else if (colIndex == atomSymbol)
{
atom.Symbol = field;
}
else if (colIndex == atomRealX)
{
hasCartesian = true;
Debug.WriteLine("Adding x3: " + ParseIntoDouble(field));
real.X = ParseIntoDouble(field);
}
else if (colIndex == atomRealY)
{
hasCartesian = true;
Debug.WriteLine("Adding y3: " + ParseIntoDouble(field));
real.Y = ParseIntoDouble(field);
}
else if (colIndex == atomRealZ)
{
hasCartesian = true;
Debug.WriteLine("Adding x3: " + ParseIntoDouble(field));
real.Z = ParseIntoDouble(field);
}
}
if (hasCartesian)
{
Vector3 a = crystal.A;
Vector3 b = crystal.B;
Vector3 c = crystal.C;
frac = CrystalGeometryTools.CartesianToFractional(a, b, c, real);
atom.FractionalPoint3D = frac;
}
if (hasFractional)
{
atom.FractionalPoint3D = frac;
}
Debug.WriteLine($"Adding atom: {atom}");
crystal.Atoms.Add(atom);
// look up next row
line = input.ReadLine();
if (line != null)
{
line = line.Trim();
}
}
}
return(line);
}
private IChemFile ReadChemFile(IChemFile file)
{
IChemSequence seq = file.Builder.NewChemSequence();
IChemModel model = file.Builder.NewChemModel();
ICrystal crystal = null;
int lineNumber = 0;
Vector3 a, b, c;
try
{
string line = input.ReadLine();
while (line != null)
{
Debug.WriteLine($"{lineNumber++}: {line}");
if (line.StartsWith("frame:", StringComparison.Ordinal))
{
Debug.WriteLine("found new frame");
model = file.Builder.NewChemModel();
crystal = file.Builder.NewCrystal();
// assume the file format is correct
Debug.WriteLine("reading spacegroup");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
crystal.SpaceGroup = line;
Debug.WriteLine("reading unit cell axes");
Vector3 axis = new Vector3();
Debug.WriteLine("parsing A: ");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.X = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Y = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Z = FortranFormat.Atof(line);
crystal.A = axis;
axis = new Vector3();
Debug.WriteLine("parsing B: ");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.X = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Y = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Z = FortranFormat.Atof(line);
crystal.B = axis;
axis = new Vector3();
Debug.WriteLine("parsing C: ");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.X = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Y = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Z = FortranFormat.Atof(line);
crystal.C = axis;
Debug.WriteLine($"Crystal: {crystal}");
a = crystal.A;
b = crystal.B;
c = crystal.C;
Debug.WriteLine("Reading number of atoms");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
int atomsToRead = int.Parse(line, NumberFormatInfo.InvariantInfo);
Debug.WriteLine("Reading no molecules in assym unit cell");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
int Z = int.Parse(line, NumberFormatInfo.InvariantInfo);
crystal.Z = Z;
string symbol;
double charge;
Vector3 cart;
for (int i = 1; i <= atomsToRead; i++)
{
cart = new Vector3();
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
symbol = line.Substring(0, line.IndexOf(':'));
charge = double.Parse(line.Substring(line.IndexOf(':') + 1), NumberFormatInfo.InvariantInfo);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
cart.X = double.Parse(line, NumberFormatInfo.InvariantInfo); // x
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
cart.Y = double.Parse(line, NumberFormatInfo.InvariantInfo); // y
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
cart.Z = double.Parse(line, NumberFormatInfo.InvariantInfo); // z
IAtom atom = file.Builder.NewAtom(symbol);
atom.Charge = charge;
// convert Cartesian coords to fractional
Vector3 frac = CrystalGeometryTools.CartesianToFractional(a, b, c, cart);
atom.FractionalPoint3D = frac;
crystal.Atoms.Add(atom);
Debug.WriteLine($"Added atom: {atom}");
}
model.Crystal = crystal;
seq.Add(model);
}
else
{
Debug.WriteLine("Format seems broken. Skipping these lines:");
while (line != null && !line.StartsWith("frame:", StringComparison.Ordinal))
{
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
}
Debug.WriteLine("Ok, resynched: found new frame");
}
}
file.Add(seq);
}
catch (Exception exception)
{
if (!(exception is IOException || exception is ArgumentException))
{
throw;
}
string message = "Error while parsing CrystClust file: " + exception.Message;
Trace.TraceError(message);
Debug.WriteLine(exception);
throw new CDKException(message, exception);
}
return(file);
}
private void processAtomLoopBlock(System.String firstLine)
{
int atomLabel = -1; // -1 means not found in this block
int atomSymbol = -1;
int atomFractX = -1;
int atomFractY = -1;
int atomFractZ = -1;
int atomRealX = -1;
int atomRealY = -1;
int atomRealZ = -1;
System.String line = firstLine.Trim();
int headerCount = 0;
bool hasParsableInformation = false;
while (line != null && line[0] == '_')
{
headerCount++;
if (line.Equals("_atom_site_label") || line.Equals("_atom_site_label_atom_id"))
{
atomLabel = headerCount;
hasParsableInformation = true;
//logger.info("label found in col: " + atomLabel);
}
else if (line.StartsWith("_atom_site_fract_x"))
{
atomFractX = headerCount;
hasParsableInformation = true;
//logger.info("frac x found in col: " + atomFractX);
}
else if (line.StartsWith("_atom_site_fract_y"))
{
atomFractY = headerCount;
hasParsableInformation = true;
//logger.info("frac y found in col: " + atomFractY);
}
else if (line.StartsWith("_atom_site_fract_z"))
{
atomFractZ = headerCount;
hasParsableInformation = true;
//logger.info("frac z found in col: " + atomFractZ);
}
else if (line.Equals("_atom_site.Cartn_x"))
{
atomRealX = headerCount;
hasParsableInformation = true;
//logger.info("cart x found in col: " + atomRealX);
}
else if (line.Equals("_atom_site.Cartn_y"))
{
atomRealY = headerCount;
hasParsableInformation = true;
//logger.info("cart y found in col: " + atomRealY);
}
else if (line.Equals("_atom_site.Cartn_z"))
{
atomRealZ = headerCount;
hasParsableInformation = true;
//logger.info("cart z found in col: " + atomRealZ);
}
else if (line.Equals("_atom_site.type_symbol"))
{
atomSymbol = headerCount;
hasParsableInformation = true;
//logger.info("type_symbol found in col: " + atomSymbol);
}
else
{
//logger.warn("Ignoring atom loop block field: " + line);
}
line = input.ReadLine().Trim();
}
if (hasParsableInformation == false)
{
//logger.info("No parsable info found");
skipUntilEmptyOrCommentLine(line);
}
else
{
// now that headers are parsed, read the data
while (line != null && line.Length > 0 && line[0] != '#')
{
//logger.debug("new row");
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
if (tokenizer.Count < headerCount)
{
//logger.warn("Column count mismatch; assuming continued on next line");
//logger.debug("Found #expected, #found: " + headerCount + ", " + tokenizer.Count);
tokenizer = new SupportClass.Tokenizer(line + input.ReadLine());
}
int colIndex = 0;
// process one row
IAtom atom = crystal.Builder.newAtom("C");
Point3d frac = new Point3d();
Point3d real = new Point3d();
bool hasFractional = false;
bool hasCartesian = false;
while (tokenizer.HasMoreTokens())
{
colIndex++;
System.String field = tokenizer.NextToken();
//logger.debug("Parsing col,token: " + colIndex + "=" + field);
if (colIndex == atomLabel)
{
if (atomSymbol == -1)
{
// no atom symbol found, use label
System.String element = extractFirstLetters(field);
atom.Symbol = element;
}
atom.ID = field;
}
else if (colIndex == atomFractX)
{
hasFractional = true;
frac.x = parseIntoDouble(field);
}
else if (colIndex == atomFractY)
{
hasFractional = true;
frac.y = parseIntoDouble(field);
}
else if (colIndex == atomFractZ)
{
hasFractional = true;
frac.z = parseIntoDouble(field);
}
else if (colIndex == atomSymbol)
{
atom.Symbol = field;
}
else if (colIndex == atomRealX)
{
hasCartesian = true;
//logger.debug("Adding x3: " + parseIntoDouble(field));
real.x = parseIntoDouble(field);
}
else if (colIndex == atomRealY)
{
hasCartesian = true;
//logger.debug("Adding y3: " + parseIntoDouble(field));
real.y = parseIntoDouble(field);
}
else if (colIndex == atomRealZ)
{
hasCartesian = true;
//logger.debug("Adding x3: " + parseIntoDouble(field));
real.z = parseIntoDouble(field);
}
}
if (hasCartesian)
{
Vector3d a = crystal.A;
Vector3d b = crystal.B;
Vector3d c = crystal.C;
frac = CrystalGeometryTools.cartesianToFractional(a, b, c, real);
atom.setFractionalPoint3d(frac);
}
if (hasFractional)
{
atom.setFractionalPoint3d(frac);
}
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Adding atom: " + atom);
crystal.addAtom(atom);
// look up next row
line = input.ReadLine().Trim();
}
}
}
// Private procedures
private void WriteCrystal(ICrystal crystal)
{
var title = crystal.Title;
if (title != null && title.Trim().Length > 0)
{
Writeln($"TITL {title.Trim()}");
}
else
{
Writeln("TITL Produced with CDK (http://cdk.sf.net/)");
}
Vector3 a = crystal.A;
Vector3 b = crystal.B;
Vector3 c = crystal.C;
double alength = a.Length();
double blength = b.Length();
double clength = c.Length();
double alpha = Vectors.RadianToDegree(Vectors.Angle(b, c));
double beta = Vectors.RadianToDegree(Vectors.Angle(a, c));
double gamma = Vectors.RadianToDegree(Vectors.Angle(a, b));
Write("CELL " + 1.54184.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(alength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(blength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(clength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(alpha.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Write(beta.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Write(gamma.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Writeln("ZERR " + ((double)crystal.Z).ToString("F5", NumberFormatInfo.InvariantInfo)
+ " 0.01000 0.01000 0.01000 0.0100 0.0100 0.0100");
string spaceGroup = crystal.SpaceGroup;
if (string.Equals("P1", spaceGroup, StringComparison.Ordinal))
{
Writeln("LATT -1");
}
else if (string.Equals("P 2_1 2_1 2_1", spaceGroup, StringComparison.Ordinal))
{
Writeln("LATT -1");
Writeln("SYMM 1/2+X , 1/2-Y , -Z");
Writeln("SYMM -X , 1/2+Y , 1/2-Z");
Writeln("SYMM 1/2-X , -Y , 1/2+Z");
}
string elemNames = "";
string elemCounts = "";
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula(crystal);
var asortedElements = MolecularFormulaManipulator.Elements(formula).ToReadOnlyList();
foreach (var element in asortedElements)
{
string symbol = element.Symbol;
elemNames += symbol + " ".Substring(symbol.Length);
string countS = MolecularFormulaManipulator.GetElementCount(formula, element).ToString(NumberFormatInfo.InvariantInfo);
elemCounts += countS + " ".Substring(countS.Length);
}
Writeln("SFAC " + elemNames);
Writeln("UNIT " + elemCounts);
/* write atoms */
for (int i = 0; i < crystal.Atoms.Count; i++)
{
IAtom atom = crystal.Atoms[i];
Vector3 cartCoord = atom.Point3D.Value;
Vector3 fracCoord = CrystalGeometryTools.CartesianToFractional(a, b, c, cartCoord);
string symbol = atom.Symbol;
string output = symbol + (i + 1);
Write(output);
for (int j = 1; j < 5 - output.Length; j++)
{
Write(" ");
}
Write(" ");
string elemID = null;
for (int elemidx = 0; elemidx < asortedElements.Count; elemidx++)
{
var elem = asortedElements[elemidx];
if (elem.Symbol.Equals(symbol, StringComparison.Ordinal))
{
elemID = (elemidx + 1).ToString(NumberFormatInfo.InvariantInfo);
break;
}
}
Write(elemID);
Write(" ".Substring(elemID.Length));
Write(fracCoord.X.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(fracCoord.Y.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Writeln(fracCoord.Y.ToString("F5", NumberFormatInfo.InvariantInfo) + " 11.00000 0.05000");
}
Writeln("END");
}
private IChemFile readChemFile(IChemFile file)
{
IChemSequence seq = file.Builder.newChemSequence();
IChemModel model = file.Builder.newChemModel();
ICrystal crystal = null;
int lineNumber = 0;
Vector3d a, b, c;
try
{
System.String line = input.ReadLine();
while (input.Peek() != -1 && line != null)
{
//logger.debug((lineNumber++) + ": ", line);
if (line.StartsWith("frame:"))
{
//logger.debug("found new frame");
model = file.Builder.newChemModel();
crystal = file.Builder.newCrystal();
// assume the file format is correct
//logger.debug("reading spacegroup");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
crystal.SpaceGroup = line;
//logger.debug("reading unit cell axes");
Vector3d axis = new Vector3d();
//logger.debug("parsing A: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.A = axis;
axis = new Vector3d();
//logger.debug("parsing B: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.B = axis;
axis = new Vector3d();
//logger.debug("parsing C: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.C = axis;
//logger.debug("Crystal: ", crystal);
a = crystal.A;
b = crystal.B;
c = crystal.C;
//logger.debug("Reading number of atoms");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
int atomsToRead = System.Int32.Parse(line);
//logger.debug("Reading no molecules in assym unit cell");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
int Z = System.Int32.Parse(line);
crystal.Z = Z;
System.String symbol;
double charge;
Point3d cart;
for (int i = 1; i <= atomsToRead; i++)
{
cart = new Point3d();
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
symbol = line.Substring(0, (line.IndexOf(":")) - (0));
charge = System.Double.Parse(line.Substring(line.IndexOf(":") + 1));
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.x = System.Double.Parse(line); // x
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.y = System.Double.Parse(line); // y
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.z = System.Double.Parse(line); // z
IAtom atom = file.Builder.newAtom(symbol);
atom.setCharge(charge);
// convert cartesian coords to fractional
Point3d frac = CrystalGeometryTools.cartesianToFractional(a, b, c, cart);
atom.setFractionalPoint3d(frac);
crystal.addAtom(atom);
//logger.debug("Added atom: ", atom);
}
model.Crystal = crystal;
seq.addChemModel(model);
}
else
{
//logger.debug("Format seems broken. Skipping these lines:");
while (!line.StartsWith("frame:") && input.Peek() != -1 && line != null)
{
line = input.ReadLine();
//logger.debug(lineNumber++ + ": ", line);
}
//logger.debug("Ok, resynched: found new frame");
}
}
file.addChemSequence(seq);
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String message = "Error while parsing CrystClust file: " + exception.Message;
//logger.error(message);
//logger.debug(exception);
throw new CDKException(message, exception);
}
return(file);
}
